Skip to content

Commit

Permalink
change default location code in fhir bundle to unknown topography (#7205
Browse files Browse the repository at this point in the history 
)

* change tests

* fix ndjson

* one more
  • Loading branch information
@fzhao99
fzhao99 authored Jan 29, 2024
1 parent 46d5fe2 commit b641485
Show file tree
Hide file tree
Showing 10 changed files with 42 additions and 47 deletions.
7 changes: 3 additions & 4 deletions backend/src/main/java/gov/cdc/usds/simplereport/api/model/TestEventExport.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -75,13 +75,12 @@ public TestEventExport(TestEvent testEvent, String processingModeCode) {
}

private String genderUnknown = "U";
public static final String DEFAULT_LOCATION_CODE = "53342003"; // http://snomed.info/id/53342003
// "Internal nose structure"
// values pulled from
public static final String DEFAULT_LOCATION_CODE = "87100004"; // http://snomed.info/id/87100004
// Topography unknown (body structure)
// https://github.com/CDCgov/prime-data-hub/blob/master/prime-router/metadata/valuesets/common.valuesets

public static final String DEFAULT_LOCATION_NAME =
"Internal nose structure (body structure)"; // http://snomed.info/id/53342003
"Topography unknown (body structure)"; // http://snomed.info/id/87100004

private final Map<String, String> genderMap =
Map.of(
Expand Down
18 changes: 7 additions & 11 deletions backend/src/test/java/gov/cdc/usds/simplereport/api/converter/FhirConverterTest.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -604,8 +604,8 @@ void convertToSpecimen_Strings_valid() {
ConvertToSpecimenProps.builder()
.specimenCode("258500001")
.specimenName("Nasopharyngeal swab")
.collectionCode("53342003 but not the default one")
.collectionName("Internal nose structure (body structure) but not the default one")
.collectionCode(DEFAULT_LOCATION_CODE + " but not the default one")
.collectionName(DEFAULT_LOCATION_NAME + " but not the default one")
.id("id-123")
.identifier("uuid-123")
.collectionDate(collectionDate)
Expand All @@ -623,9 +623,9 @@ void convertToSpecimen_Strings_valid() {
assertThat(actual.getCollection().getBodySite().getCodingFirstRep().getSystem())
.isEqualTo(snomedCode);
assertThat(actual.getCollection().getBodySite().getCodingFirstRep().getCode())
.isEqualTo("53342003 but not the default one");
.isEqualTo(DEFAULT_LOCATION_CODE + " but not the default one");
assertThat(actual.getCollection().getBodySite().getText())
.isEqualTo("Internal nose structure (body structure) but not the default one");
.isEqualTo(DEFAULT_LOCATION_NAME + " but not the default one");
assertThat(((DateTimeType) actual.getCollection().getCollected()).getValue())
.isEqualTo("2023-06-22T16:38:00Z");
}
Expand All @@ -648,10 +648,7 @@ void convertToSpecimen_Strings_null() {
void convertToSpecimen_SpecimenType_valid() {
var specimenType =
new SpecimenType(
"Nasopharyngeal swab",
"258500001",
"Internal nose structure (body structure)",
"53342003");
"Nasopharyngeal swab", "258500001", DEFAULT_LOCATION_NAME, DEFAULT_LOCATION_CODE);
var internalId = UUID.randomUUID();
ReflectionTestUtils.setField(specimenType, "internalId", internalId);

Expand All @@ -673,9 +670,8 @@ void convertToSpecimen_SpecimenType_valid() {
assertThat(actual.getCollection().getBodySite().getCodingFirstRep().getSystem())
.isEqualTo(snomedCode);
assertThat(actual.getCollection().getBodySite().getCodingFirstRep().getCode())
.isEqualTo("53342003");
assertThat(actual.getCollection().getBodySite().getText())
.isEqualTo("Internal nose structure (body structure)");
.isEqualTo(DEFAULT_LOCATION_CODE);
assertThat(actual.getCollection().getBodySite().getText()).isEqualTo(DEFAULT_LOCATION_NAME);
assertThat(((DateTimeType) actual.getCollection().getCollected()).getValue())
.isEqualTo("2023-06-22T13:16:00.00Z");
assertThat(actual.getReceivedTimeElement().getValueAsString())
Expand Down
4 changes: 2 additions & 2 deletions backend/src/test/resources/fhir/bundle.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -325,10 +325,10 @@
"coding": [
{
"system": "http://snomed.info/sct",
"code": "53342003"
"code": "87100004"
}
],
"text": "Internal nose structure (body structure)"
"text": "Topography unknown (body structure)"
},
"collectedDateTime": "2023-07-14T15:45:34+00:00"
}
Expand Down
20 changes: 10 additions & 10 deletions backend/src/test/resources/fhir/bundles-upload-integration-testing.ndjson
View file
Original file line number Diff line number Diff line change
Expand Up @@ -350,10 +350,10 @@
"coding": [
{
"system": "http://snomed.info/sct",
"code": "53342003"
"code": "87100004"
}
],
"text": "Internal nose structure (body structure)"
"text": "Topography unknown (body structure)"
}
}
}
Expand Down Expand Up @@ -1179,10 +1179,10 @@
"coding": [
{
"system": "http://snomed.info/sct",
"code": "53342003"
"code": "87100004"
}
],
"text": "Internal nose structure (body structure)"
"text": "Topography unknown (body structure)"
}
}
}
Expand Down Expand Up @@ -1735,10 +1735,10 @@
"coding": [
{
"system": "http://snomed.info/sct",
"code": "53342003"
"code": "87100004"
}
],
"text": "Internal nose structure (body structure)"
"text": "Topography unknown (body structure)"
}
}
}
Expand Down Expand Up @@ -2335,10 +2335,10 @@
"coding": [
{
"system": "http://snomed.info/sct",
"code": "53342003"
"code": "87100004"
}
],
"text": "Internal nose structure (body structure)"
"text": "Topography unknown (body structure)"
}
}
}
Expand Down Expand Up @@ -2891,10 +2891,10 @@
"coding": [
{
"system": "http://snomed.info/sct",
"code": "53342003"
"code": "87100004"
}
],
"text": "Internal nose structure (body structure)"
"text": "Topography unknown (body structure)"
}
}
}
Expand Down
4 changes: 2 additions & 2 deletions backend/src/test/resources/fhir/specimen.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,10 +15,10 @@
"coding": [
{
"system": "http://snomed.info/sct",
"code": "53342003"
"code": "87100004"
}
],
"text": "Internal nose structure (body structure)"
"text": "Topography unknown (body structure)"
},
"collectedDateTime": "2023-06-22T11:35:00-04:00"
},
Expand Down
8 changes: 4 additions & 4 deletions backend/src/test/resources/testResultUpload/fhir-for-csv-with-comments.ndjson
View file
Original file line number Diff line number Diff line change
Expand Up @@ -350,10 +350,10 @@
"coding": [
{
"system": "http://snomed.info/sct",
"code": "53342003"
"code": "87100004"
}
],
"text": "Internal nose structure (body structure)"
"text": "Topography unknown (body structure)"
}
}
}
Expand Down Expand Up @@ -1183,10 +1183,10 @@
"coding": [
{
"system": "http://snomed.info/sct",
"code": "53342003"
"code": "87100004"
}
],
"text": "Internal nose structure (body structure)"
"text": "Topography unknown (body structure)"
}
}
}
Expand Down
4 changes: 2 additions & 2 deletions backend/src/test/resources/testResultUpload/fhir-for-csv-with-flu-only.ndjson
View file
Original file line number Diff line number Diff line change
Expand Up @@ -350,10 +350,10 @@
"coding": [
{
"system": "http://snomed.info/sct",
"code": "53342003"
"code": "87100004"
}
],
"text": "Internal nose structure (body structure)"
"text": "Topography unknown (body structure)"
}
}
}
Expand Down
8 changes: 4 additions & 4 deletions backend/src/test/resources/testResultUpload/fhir-for-csv-with-specimenType-loinc.ndjson
View file
Original file line number Diff line number Diff line change
Expand Up @@ -350,10 +350,10 @@
"coding": [
{
"system": "http://snomed.info/sct",
"code": "53342003"
"code": "87100004"
}
],
"text": "Internal nose structure (body structure)"
"text": "Topography unknown (body structure)"
}
}
}
Expand Down Expand Up @@ -1183,10 +1183,10 @@
"coding": [
{
"system": "http://snomed.info/sct",
"code": "53342003"
"code": "87100004"
}
],
"text": "Internal nose structure (body structure)"
"text": "Topography unknown (body structure)"
}
}
}
Expand Down
4 changes: 2 additions & 2 deletions backend/src/test/resources/testResultUpload/test-results-upload-valid-as-fhir.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -350,10 +350,10 @@
"coding": [
{
"system": "http://snomed.info/sct",
"code": "53342003"
"code": "87100004"
}
],
"text": "Internal nose structure (body structure)"
"text": "Topography unknown (body structure)"
}
}
}
Expand Down
Loading

0 comments on commit b641485

Please sign in to comment.